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Table 5 Expectations and estimates of the proportion of variance explained by the variants in different MAF classes using imputed sequence data for the feet and legs trait

From: Contribution of rare and low-frequency whole-genome sequence variants to complex traits variation in dairy cattle

  MAF class
0.001–0.01 0.01–0.05 0.05–0.1 0.1–0.2 0.2–0.3 0.3–0.4 0.4–0.5
Expectation VR1a 0.006 0.065 0.079 0.252 0.210 0.194 0.193
Expectation VR2a 0.147 0.186 0.134 0.169 0.132 0.118 0.114
Estimateb 0.059 0.149 0.025 0.053 0.299 0.417 0.002
  1. All proportions are scaled to sum to 1 across all MAF classes
  2. aExpectations of the proportion of variance explained based on the assumption of VanRaden’s methods 1 (VR1) and 2 (VR2); see [21]
  3. bEstimated proportion of DRP variance explained for feet and legs using the GREML-MS method with partitioning of imputed sequence variants into seven MAF groups